Difference between revisions of "Web Services REST API"

Revision as of 18:21, 15 March 2016

Our web services let you incorporate CoGe's database of organisms, genomes, and other data sets into your web site or pipeline.

Documentation

• Interactive documentation: https://genomevolution.org/r/apidocs
• Specification document: http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc
• Embedding CoGe JBrowse in another website
• Automated Testing (Robot Framework): https://geco.iplantcollaborative.org/coge/test/log.html

Examples

Organism Search

curl https://genomevolution.org/coge/api/v1/organisms/search/col-0
[
{
   "organisms":
      [
         {
            "id": "1",
            "name": "Arabidopsis thaliana Col-0 (thale cress)",    
            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis"
         }
      ]
}

curl https://genomevolution.org/coge/api/v1/genomes/search/col-0
    {
    "name": "",
    "chromosome_count": 7,
    "sequence_type": {
    "id": "1",
    "description": "unmasked sequence data",
    "name": "unmasked"
    },
"info": "Arabidopsis thaliana Col-0 (thale cress) (v10.02, id16911): unmasked",
"description": "",
"organism": {
"id": 1,
"description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis",
"name": "Arabidopsis thaliana Col-0 (thale cress)"
},
    "restricted": false,
    "organism_id": 1,
    "version": "10.02",
    "id": 16911,
    "link": ""
    },
    ...
]

Genome Fetch

curl https://genomevolution.org/coge/api/v1/genomes/16911
{
   "id": 16911
   "name": "",
   "description": "",
   "version": "10.02",
   "link": "",
   "restricted": false,
   "sequence_type": {
      "name": "unmasked",
      "description": "unmasked sequence data"
   },
   "experiments": [31,32,33, ...],
   "metadata": [],
}

More examples to be added soon!